Wikidata:Property proposal/GTDB taxon

GTDB taxon

Originally proposed at Wikidata:Property proposal/Natural science

   Not done

Description	Taxonomic identifier in the Genome Taxonomy Database, a proposed phylogenomic nomenclature of prokaryotes
Represents	Genome Taxonomy Database (Q104830506)
Data type	External identifier
Domain	prokaryotes (Q19081)
Allowed values	[dpcofgs]__[A-Z][-[:alnum:]_ ]*
Example 1	Paenarthrobacter ureafaciens (Q55180430) → s__Paenarthrobacter ureafaciens
Example 2	CPR group (Q27110262) → p__Patescibacteria
Example 3	Asgard (Q45003302) → p__Asgardarchaeota
Example 4	Clostridia (Q132809) → c__Clostridia; c__Clostridia_A
Example 5	Escherichia coli (Q25419) → s__Escherichia coli; s__Escherichia coli_C; s__Escherichia coli_D; s__Escherichia dysenteriae; s__Escherichia fergusonii; s__Escherichia flexneri
Source	see Q104830506#P1343
Number of IDs in source	> 45,000 (45,416 as of r85)
Expected completeness	eventually complete (Q21873974)
Formatter URL	https://gtdb.ecogenomic.org/tree?r=$1
Robot and gadget jobs	maybe
Applicable "stated in"-value	Genome Taxonomy Database (Q104830506)
Distinct-values constraint	no
Wikidata project	WikiProject Taxonomy (Q8503033)

Motivation

The GTDB provides a "clean", if unorthodox, tree of life without paraphyletic or oddly-ranked groups. It is especially helpful to provide GTDB links on taxa that are known to be weird themselves or include such taxa. Artoria2e5 (talk) 05:40, 2 February 2021 (UTC)

Discussion

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•  Comment @Artoria2e5: I attempted to link your examples, but the space character breaks linking. How do you plan to handle the ID's with space characters in them? ArthurPSmith (talk) 22:21, 2 February 2021 (UTC)
  • @ArthurPSmith:, you are supposed to handle them like a browser does, i.e. do an urlencode to turn spaces into %20. See https://gtdb.ecogenomic.org/tree?r=s__Paenarthrobacter%20ureafaciens. --Artoria2e5 (talk) 22:28, 2 February 2021 (UTC)
    • Ok, so leave them as spaces in the ID's then? Maybe you should take care of the linking (see other proposals for external id properties). ArthurPSmith (talk) 22:33, 2 February 2021 (UTC)
      • Yes, leave them as spaces: I think the $1 thing does that automatically. I will add the links... now. --Artoria2e5 (talk) 07:53, 5 February 2021 (UTC)
• I don't see why Escherichia dysenteriae and Escherichia fergusonii are given as examples for E. coli. They are different species. UWashPrincipalCataloger (talk) 01:05, 5 April 2021 (UTC)
•  Not done - no support for the proposal --DannyS712 (talk) 01:27, 2 January 2022 (UTC)